criteria for distinguishing parthood from spatial inclusion in biological objects

Criteria for distinguishing parthood from spatial

inclusion in biological objects

Stefan Schulz, Philipp DaumkeDepartment of Medical Informatics

University Hospital Freiburg (Germany)

Beyond Part-Of

Part-of / has-part: Generally accepted foundational

relation to describe the spatial composition of

biological organisms

Can the generic part-of be clearly distinguished from

other relations by non-discretionary criteria ?

Is the part-of relation suitable for an ontology of

biological systems ?

Phagocytosis / Digestion

Virus

Cell

t1 t2 t3 t4 t5

Secretion

t1 t2 t3 t4 t5

Parthood and Spatial Inclusionpart-of : p (x, y, t) generic parthood relation between objects Region: R(z) z is a region in (Euklidean) space

z = r (x, t) z is the region where x is located at t p (x, y, t) p (r (x ,t), r (y, t))

(Donnelly, IJCAI 03)Spatial inclusion (coverage, (partly) location,… )si spatially included by: si (x, y, t) =def p (r (x, t), r (y ,t))

When does inclusion imply parthood ? Under which circumstances can we

infer parthood from spatial inclusion ?

Sortal constraints Life cycle Ontological Dependence Function

si (x, y, t) p (x, y, t)

1. Sortal Constraints

x and y are regions: R(x) R(y) si (x, y) p (x, y)

x is material, y is immaterial:Solid (x) Hole (y) si (x, y) p (x, y) si (myBrain, myCranialCavity) p (myBrain, myCranialCavity)

x is an non-biological artifact: si (myPacemaker, myBody) p (myPacemaker, myBody)

si (myInlay, myTooth) p (myInlay, myTooth)

si (aBullet, myArm) p (aBullet, myArm)

+

–

–

1. Sortal Constraints

Alien organisms (and what they spatially

include)

Symbionts: si (anEcoliBacterium , myIntestine) p (anEcoliBacterium , myIntestine)

Parasites: si (anEchinococcus, myLiver) p (anEchinococcus, myLiver)

Preys: si (anElephant, aSnake) p (anElephant, aSnake)

Embryos, Fetuses: si (Leonardo, Caterina) p (Leonardo, Caterina)

–

–

–

–

1. Sortal ConstraintsBorderline cases (I)

Grafts, transplants, transfusions

autologous: si (mySaphenousVein, myHeart) p (mySaphenousVein, myHeart)

homologous: si (thisTransfusedRBC, myBlood) p (thisTransfusedRBC, myBlood)

heterologous: si (thisPigValve, myHeart) p (thisPigValve, myHeart)

?

?

?

1. Sortal ConstraintsBorderline cases (II)

Masses and Collections

Body Fluids (constant exchange but few discharge)

… as a whole (endure over time) si (myCSF, myCNS) p (myCSF, myCNS)

… ad hoc (momentaneous existence) si (thisAmountOfCSF, myFourthVentricle) p (thisAmountOfCSF, myFourthVentricle)

Body Secretions (periodic discharge): si (thisAmountOfUrine, myBladder) p (thisAmountOfUrine, myBladder)

Other cases: si (myLung, thisVolumeOfAir)

si (thisCOllectionOfLeukozytes, myGastricMucosa)

?

–

–

–

2. Life Cycle t

pre-inclusion inclusion post inclusion

s si (x,y)

x

xx

xy

xp (aFingertip, aFinger)

x

x

p (myHead, myBody)

p (aK+Ion, aHeartMuscleCell)

–

p (anInsuline Molecule, aPancreaticBetaCell)

p (a CaHA crystal, aBone)

+

+

?

p (aLung,

anN2Molecule)–

p (anAlaninMolecule, myBody)?

+

Which patternsallow the inferencefrom inclusion to part ?

2. Life Cycle: Case studyx

si (anAlaninMolecule, anAnimalBody)

Ingested contained as ingredient of a bone, digestedand used for albumin synthesis. Albumin excreted by urine

Ingested contained as ingredient of vegetal fibers, excreted by feces without digestion

Ingested, metabolized and used for collagen synthesis. Integrated in the structure of a bone

Synthesized in the liver, built in a hemoglobin molecule,leaves body by bleeding

Synthesized in the liver, built into a globulin molecule,then catabolized in a cell

Included in the zygote and the early embryo. Then catabolized in the maternal organism

3. Ontological Dependency

Individual levelx can only exist when y exists: Boundaries, non-detachable objects: si (myLiverSurface , myLiver) p (myLiverSurface , myLiver)

si (mySkull, MyHead) p (myLiverSurface , myLiver)

Identity-bearing Objects si (myBrain, MyHead) p (myBrain , myHead)

Class levelx can only exist if an instance of the class Y exists

x: is-a (x, Cell) y: is-a (y, H2O) si-1(x, y)

+

+

–Does not allow the inference from inclusion to part!

4. Function

Preliminary sketch:

If x is missing, then a function of y cannot be realized:Example: If a kidney is missing, then the filtration function of the bodycannot be realized.Hence, a transplanted kidney, which has this function, can be considered part-of the receptor organism.

Conclusion Parthood implies Spatial inclusion What differentiates Parthood in biological organisms ? Workflow of analyses needed:

1. Check sortal constraints2. Analyze life cycle3. Analyse ontological dependency4. Analyse function (?)

Unclear cases remain ! Implication for biological ontologies:

Use Spatial inclusion as primitive instead of Parthood Automatic Refinement to Parthood where the above workflow

yields unambiguous results

Anatomical boundaries and

immaterial objects

Stefan SchulzDepartment of Medical Informatics

University Hospital Freiburg (Germany)

Is the fly inside or outside her body ?

Problem (I)

Biological objects need clearly defined

boundaries to enable assertions

parthood and location

Most Biological objects are sponge-like

(full of vessels, capillaries, cavities,

holes

and other hollow spaces)

http://faculty.une.edu/com/abell/histo/histolab2.htm

Problem (II)

Many cavities communicate with the

exterior space (e.g. respiratory system)

Common conceptualization (cf.

biomedical terminologies): biological

objects have immaterial parts, eg.

Lumen of esophagus, alveolar lumen,

many cavities and holes in bones, …

How to deal with hollow spaces ?

S S

B BH H

E

H is part of E, hence B is located outside of S

H is part of S, hence B is located inside of S

Problem

Inside or outside ? Example: Bronchi

A foreign body in a bronchus is in the lung

Strict topological viewconflicts with shared conceptualization

B

Where to delimit ?

1. All hollow spaces are part of the exterior…

… but nothing can be located inside…

2. Those hollow spaces which communi-cate with the exterior are part of the exterior space…

… what if some spaces only temporarily communicate ?

4. The complete convex hull is part of the object…

… then the body would practically spatially coincide with the vascular system !

3. Only those hollow spaces which are containers something are part of the exterior space…

… how to ascertain whether they are containers ?

Solution

… how to ascertain whether they are containers ?

GlandCryptVillus

Algebraic Properties: Part-Of / Has-Part vs. part-of / has-part Instance level :

part-of (a, b), part-of (b, c) part-of (a, c) Transitivity ? part-of (a, b) part-of (b, a) Asymmetry part-of (a, b) a b Irreflexivity ?

part-of (a, b) has-part (b, a) Inverse Relation

Class level*:Part-For (A, B), Part-For (B, C) Part-For (A, C) Part-For (A, B) Part-For (B, A) Part-For (A, B) Is-A (A, B) ? Part-For (B, A) does not necessarily imply Has-Part (A, B)Possible-Part (B, A) implies Has-Possible-Part (A, B)(…)

Part-Of in Anatomies: Consensus required about

Domain and range of part-of relations

Algebraic properties of part-of relations

Intended meaning of part-of relations in

the domain of biology and medicine

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

Parts as Components

part-of (Finger, Hand)

part-of (Bone Marrow, Bone)

part-of (Sodium Ion, Cytoplasm) ?

part-of (Sarcomer, Muscle)

part-of (Heart, Human Body)

Parts “build” the whole

“Intuitive” notion of part. Controversial

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

Parts as Functional Components

part-of (Finger, Hand) part-of (Lymph Node, Lymphatic System)

part-of (Cell Nucleus, Cell)

part-of (Tendon, Muscle )

part-of (Tooth, Jaw)

Part contributes to thefunction of the whole

More restricted, may conflict with notions of connection

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

no clear distinction !

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

Continuous exchange of matter

Endosymbiont Hypothesis

2.5 billion years ago: Primitive cell with bacterium-like symbionts

Today: Chloroplasts (Plants) Mitochondria

Are the organells part of the cell

Which eggs arepart of the body ?

Topological parts

part-of (Mitochondrium, Cell)part-of (Brain, Head)part-of (Brain, Cranial Cavity) ?part-of (Ovum, Oviduct) ?part-of (Finger, Hand)part-of (Amount of Blood, Right Ventricle) ?

Located within the boundariesof an object

has-location instead of part-of ?

Topological parts

has-location (Mitochondrium, Cell)has-location (Brain, Head)has-location (Brain, Cranial Cavity) has-location (Ovum, Oviduct) has-location (Finger, Hand)has-location (amount of Blood, Right Ventricle)

Located within the boundariesof an object

has-location as a mereotopological primitive ?

Topological partsHow to deal with hollow spaces ?

S S

B BH H

E

H is part of E, hence B is located outside of S

H is part of S, hence B is located inside of S

Example

Inside or outside ? Example: Bronchi

A foreign body in a bronchus is in the lung

Strict topological viewconflicts with shared conceptualization

B

Different notions of part-of

Time-independent: Compositional Functional Topological

Time-dependent: a part-of b at any point of time

a part-of b at every point of time a part-of b at one point of time,

a NOT part-of b at another point of time

instance level

Example: Transplantation

K1 K2

John Paul

part-of (K1, John)part-of (K2, John)

t1 t2

Example: Transplantation

K1 K2

John Paul

part-of (K1, John)part-of (K2, John)

part-of (K2, Paul)part-of (K2, John)

?

t1 t2

Phagocytosis / Digestion

Virus

Cell

t1 t2 t3 t4 t5

Secretion

t1 t2 t3 t4 t5

Conclusion

Part-of: example, how many different interpretations co-exist

Standardization: need to eliminate ambiguity by precise characterization of foundational primitives (properties, relations)

Solid theoretical basis is needed, e.g. mereotopology: Simons, Casati, Smith, Varzi,…